Hmm wonder if two of my books are scraped incorrectly. It also picked up some old issues from 1998 in the smartlist.

That is weird. There was the limited series The X-Men vs. the Avengers by Roger Stern and Marc Silvestri but that was released back in 1987. Could the books you linked with the scrapper be reprints that came out in '98?

I will check when I get home later but I believe they were from 1998 issue 25 and 26 iirc.

Ah, that helps. If you're using the smartlist that 600WPMPO posted then you probably have Avengers (volume 1998) #25 & #26, which both were released in 2000, already in your library. So, ComicRack may think these are the issues to grab since the new issues, Avengers (volume 2010) #25 & #26 haven't been released just yet thus they aren't in your library yet.
You can probably fix this by putting in a "Volume is 2010" rule right after the rules
"Series is Avengers"
"Number is in the range 25 and 26"

Not for DC, Is there a current jumping on point for a X-Men Comic and same for Avengers? Like New Avengers if that worth reading from issue #1 and X-Men Volume 4 is its current run?

As long as you can get your hands on the back issues without too much cost, I would tend to suggest going back 2 to 3 years as a starting point so that way you get what's currently going on, plus any long term plots that may just begin coming to climax. So with the latest volume of Avengers (2010) hitting issue #25 I would most definitively start around issue #1. With X-Men, you can also start with the latest volume X-Men (2010) at issue #1. Of course both groups have other related titles like Avengers Academy, Avengers: The Initiative, New Avengers, Astonishing X-Men, Uncanny X-Men & X-Men Legacy that were going on around the same time when both of the main titles started their latest #1 run, so you could follow those books as well to get a bigger picture of what's been going on with both super hero groups.